Brain data
Contents
Brain data#
This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.
Gray matter qMRI#
Code imports#
# Python imports
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd
# Import custom tools
from tools.data import Data
from tools.plot import Plot
Download data#
data_type = 'brain'
release_version = 'latest'
dataset = Data(data_type)
dataset.download(release_version)
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Load data plot it#
dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')
fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')
[[1.4885, 1.4651, 1.285, -100], [1.4674, 1.4598, 1.4625, 1.4542], [1.4929, 1.4977, -100, 1.4964], [1.315, 1.2597, 1.2551, -100], [1.4773, 1.4801, -100, -100], [-100, -100, -100, 1.3065]]
MP2RAGE
[[1.7582, 1.7805, 1.5235, -100], [1.8387, 1.7777, 1.6814, 1.6291], [1.7867, 1.83, -100, 1.7999], [1.4853, 1.3929, 1.4778, -100], [1.9455, 1.8808, -100, -100], [-100, -100, -100, 1.5384]]
MTS
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
MTR
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
MTsat
[[1.4885, 1.4651, 1.285, -100], [1.4674, 1.4598, 1.4625, 1.4542], [1.4929, 1.4977, -100, 1.4964], [1.315, 1.2597, 1.2551, -100], [1.4773, 1.4801, -100, -100], [-100, -100, -100, 1.3065]]
[[1.7582, 1.7805, 1.5235, -100], [1.8387, 1.7777, 1.6814, 1.6291], [1.7867, 1.83, -100, 1.7999], [1.4853, 1.3929, 1.4778, -100], [1.9455, 1.8808, -100, -100], [-100, -100, -100, 1.5384]]
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
[[ 1.4885 1.4651 1.285 -100. ]
[ 1.4674 1.4598 1.4625 1.4542]
[ 1.4929 1.4977 -100. 1.4964]
[ 1.315 1.2597 1.2551 -100. ]
[ 1.4773 1.4801 -100. -100. ]
[-100. -100. -100. 1.3065]
[ 1.7582 1.7805 1.5235 -100. ]
[ 1.8387 1.7777 1.6814 1.6291]
[ 1.7867 1.83 -100. 1.7999]
[ 1.4853 1.3929 1.4778 -100. ]
[ 1.9455 1.8808 -100. -100. ]
[-100. -100. -100. 1.5384]]
[[ 1.4885 1.4651 1.285 -100. ]
[ 1.4674 1.4598 1.4625 1.4542]
[ 1.4929 1.4977 -100. 1.4964]
[ 1.315 1.2597 1.2551 -100. ]
[ 1.4773 1.4801 -100. -100. ]
[-100. -100. -100. 1.3065]
[ 1.7582 1.7805 1.5235 -100. ]
[ 1.8387 1.7777 1.6814 1.6291]
[ 1.7867 1.83 -100. 1.7999]
[ 1.4853 1.3929 1.4778 -100. ]
[ 1.9455 1.8808 -100. -100. ]
[-100. -100. -100. 1.5384]]
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
[[ 1.4885 1.4651 1.285 -100. ]
[ 1.4674 1.4598 1.4625 1.4542]
[ 1.4929 1.4977 -100. 1.4964]
[ 1.315 1.2597 1.2551 -100. ]
[ 1.4773 1.4801 -100. -100. ]
[-100. -100. -100. 1.3065]
[ 1.7582 1.7805 1.5235 -100. ]
[ 1.8387 1.7777 1.6814 1.6291]
[ 1.7867 1.83 -100. 1.7999]
[ 1.4853 1.3929 1.4778 -100. ]
[ 1.9455 1.8808 -100. -100. ]
[-100. -100. -100. 1.5384]]
[[ 1.4885 1.4651 1.285 -100. ]
[ 1.4674 1.4598 1.4625 1.4542]
[ 1.4929 1.4977 -100. 1.4964]
[ 1.315 1.2597 1.2551 -100. ]
[ 1.4773 1.4801 -100. -100. ]
[-100. -100. -100. 1.3065]
[ 1.7582 1.7805 1.5235 -100. ]
[ 1.8387 1.7777 1.6814 1.6291]
[ 1.7867 1.83 -100. 1.7999]
[ 1.4853 1.3929 1.4778 -100. ]
[ 1.9455 1.8808 -100. -100. ]
[-100. -100. -100. 1.5384]]
White matter qMRI#
fig_wm = Plot(dataset, plot_name = 'brain-2')
fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')
[[0.94136, 0.9462, 1.0346, -100], [0.90359, 0.90871, 0.90185, 0.90232], [0.88612, 0.88218, -100, 0.88721], [0.97833, 0.9795, 0.968, -100], [0.91238, 0.90486, -100, -100], [-100, -100, -100, 0.96392]]
MP2RAGE
[[1.0207, 1.0348, 1.0475, -100], [1.021, 1.0044, 0.99252, 0.96173], [0.97915, 0.9999, -100, 1.036], [1.0128, 0.96615, 1.028, -100], [1.0388, 1.0421, -100, -100], [-100, -100, -100, 1.0122]]
MTS
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
MTR
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
MTsat
[[0.94136, 0.9462, 1.0346, -100], [0.90359, 0.90871, 0.90185, 0.90232], [0.88612, 0.88218, -100, 0.88721], [0.97833, 0.9795, 0.968, -100], [0.91238, 0.90486, -100, -100], [-100, -100, -100, 0.96392]]
[[1.0207, 1.0348, 1.0475, -100], [1.021, 1.0044, 0.99252, 0.96173], [0.97915, 0.9999, -100, 1.036], [1.0128, 0.96615, 1.028, -100], [1.0388, 1.0421, -100, -100], [-100, -100, -100, 1.0122]]
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
[[ 0.94136 0.9462 1.0346 -100. ]
[ 0.90359 0.90871 0.90185 0.90232]
[ 0.88612 0.88218 -100. 0.88721]
[ 0.97833 0.9795 0.968 -100. ]
[ 0.91238 0.90486 -100. -100. ]
[-100. -100. -100. 0.96392]
[ 1.0207 1.0348 1.0475 -100. ]
[ 1.021 1.0044 0.99252 0.96173]
[ 0.97915 0.9999 -100. 1.036 ]
[ 1.0128 0.96615 1.028 -100. ]
[ 1.0388 1.0421 -100. -100. ]
[-100. -100. -100. 1.0122 ]]
[[ 0.94136 0.9462 1.0346 -100. ]
[ 0.90359 0.90871 0.90185 0.90232]
[ 0.88612 0.88218 -100. 0.88721]
[ 0.97833 0.9795 0.968 -100. ]
[ 0.91238 0.90486 -100. -100. ]
[-100. -100. -100. 0.96392]
[ 1.0207 1.0348 1.0475 -100. ]
[ 1.021 1.0044 0.99252 0.96173]
[ 0.97915 0.9999 -100. 1.036 ]
[ 1.0128 0.96615 1.028 -100. ]
[ 1.0388 1.0421 -100. -100. ]
[-100. -100. -100. 1.0122 ]]
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
[[ 0.94136 0.9462 1.0346 -100. ]
[ 0.90359 0.90871 0.90185 0.90232]
[ 0.88612 0.88218 -100. 0.88721]
[ 0.97833 0.9795 0.968 -100. ]
[ 0.91238 0.90486 -100. -100. ]
[-100. -100. -100. 0.96392]
[ 1.0207 1.0348 1.0475 -100. ]
[ 1.021 1.0044 0.99252 0.96173]
[ 0.97915 0.9999 -100. 1.036 ]
[ 1.0128 0.96615 1.028 -100. ]
[ 1.0388 1.0421 -100. -100. ]
[-100. -100. -100. 1.0122 ]]
[[ 0.94136 0.9462 1.0346 -100. ]
[ 0.90359 0.90871 0.90185 0.90232]
[ 0.88612 0.88218 -100. 0.88721]
[ 0.97833 0.9795 0.968 -100. ]
[ 0.91238 0.90486 -100. -100. ]
[-100. -100. -100. 0.96392]
[ 1.0207 1.0348 1.0475 -100. ]
[ 1.021 1.0044 0.99252 0.96173]
[ 0.97915 0.9999 -100. 1.036 ]
[ 1.0128 0.96615 1.028 -100. ]
[ 1.0388 1.0421 -100. -100. ]
[-100. -100. -100. 1.0122 ]]